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The interior surface of the jejunum—which is exposed to ingested food—is covered in finger-like projections of mucosa, called villi, which increase the surface area of tissue available to absorb nutrients from ingested foodstuffs. The epithelial cells which line these villi have microvilli. The transport of nutrients across epithelial cells through the jejunum and ileum includes the passive transport of sugar fructose and the active transport of amino acids, small peptides, vitamins, and most glucose. The villi in the jejunum are much longer than in the duodenum or ileum.

The pH in the jejunum is usually between 7 and 9 (neutral or slightly alkaline).

The jejunum and the ileum are suspended by mesentery which gives the bowel great mobility within the abdomen. It also contains circular and longitudinal smooth muscle which helps to move food along by a process known as peristalsis.

If the jejunum is impacted by blunt force the emesis reflex (vomiting) will be initiated.[6]

The jejunum contains very few Brunner's glands (found in the duodenum) or Peyer's patches (found in the ileum). However, there are a few jejunal lymph nodes suspended in its mesentery. The jejunum has many large circular folds in its submucosa called plicae circulares which increase the surface area for nutrient absorption. The plicae circulares are the best developed in the jejunum.

There is no line of demarcation between the jejunum and the ileum. However, there are subtle histological differences:

The jejunum has less fat inside its mesentery than the ileum.

The jejunum is typically of larger diameter than the ileum.

The villi of the jejunum look like long, finger-like projections, and are a histologically identifiable structure.

The lining of the jejunum is specialized for the absorption, by enterocytes, of small nutrient particles which have been previously digested by enzymes in the duodenum. Once absorbed, nutrients (with the exception of fat, which goes to the lymph) pass from the enterocytes into the enterohepatic circulation and enter the liver via the hepatic portal vein, where the blood is processed.[7] The jejunum is involved in magnesium absorption[citation needed].